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Immortalin / peptide-shaker

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Importing Data Canceled - Attempting to create duplicate peptide key #56

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
> What steps will reproduce the problem?

We loaded 12 result files produced by Searchgui (MS-GF+) into PeptideShaker.
After about 2 hours of analysis, with PeptideShaker at more than 80% of the 
total progress, in the log window it says 'importing data cancelled' and starts 
a cancellation process. The process seems to hang or stop.

The last part of the report file is:
...
...
Wed Nov 12 14:08:54 KST 2014        26085 conflicts resolved. 12743 protein 
groups remaining (140 suspicious).
Wed Nov 12 14:08:54 KST 2014        Correcting protein probabilities.
Wed Nov 12 14:08:54 KST 2014        Saving protein probabilities.
Wed Nov 12 14:08:54 KST 2014        Validating identifications at 1% FDR, 
quality control of matches.
Wed Nov 12 14:09:59 KST 2014        Scoring PTMs in peptides.

Wed Nov 12 14:10:00 KST 2014        Importing Data Canceled!
Wed Nov 12 14:10:00 KST 2014        An error occured while loading the 
identification files:
Wed Nov 12 14:10:00 KST 2014        Attempting to create duplicate peptide key: 
RIHMEKEMEMKK_15.994915-ATAA-4.

> What version of the product are you using? On what operating system?

PeptideShaker 0.35.1
SearchGUI-1.22.2
Windows 7 Professional 64bit (8 GB RAM)
Java 1.8.0_25

> Please provide any additional information below.

> If the reported issue resulted in the tool crashing, please
> also upload the file called PeptideShaker.log (found in the
> PeptideShaker-X.Y.Z\resources folder).

Wed Nov 12 11:46:27 KST 2014: PeptideShaker version 0.35.1.
Memory given to the Java virtual machine: 7456948224.
Total amount of memory in the Java virtual machine: 128974848.
Free memory: 110682088.
Java version: 1.8.0_25.
1714 script command tokens
(C) 2009 Jmol Development
Jmol Version: 12.0.43  2011-05-03 14:21
java.vendor: Oracle Corporation
java.version: 1.8.0_25
os.name: Windows 7
memory: 30.5/129.0
processors available: 4
useCommandThread: false
<CompomicsError>PeptideShaker processing failed. See the PeptideShaker log for 
details.</CompomicsError>
java.lang.IllegalArgumentException: Attempting to create duplicate peptide key: 
RIHMEKEMEMKK_15.994915-ATAA-4.
    at eu.isas.peptideshaker.ptm.PtmScorer.scorePTMs(PtmScorer.java:823)
    at eu.isas.peptideshaker.ptm.PtmScorer.scorePeptidePtms(PtmScorer.java:1306)
    at eu.isas.peptideshaker.PeptideShaker.processIdentifications(PeptideShaker.java:453)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:554)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:454)
    at javax.swing.SwingWorker$1.call(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at javax.swing.SwingWorker.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
Free memory: 2340545688

Wed Nov 12 14:25:20 KST 2014: PeptideShaker version 0.35.1.
Memory given to the Java virtual machine: 7456948224.
Total amount of memory in the Java virtual machine: 128974848.
Free memory: 110680088.
Java version: 1.8.0_25.
1714 script command tokens
(C) 2009 Jmol Development
Jmol Version: 12.0.43  2011-05-03 14:21
java.vendor: Oracle Corporation
java.version: 1.8.0_25
os.name: Windows 7
memory: 30.2/129.0
processors available: 4
useCommandThread: false

Original issue reported on code.google.com by Jihye.Sh...@gmail.com on 12 Nov 2014 at 5:29

GoogleCodeExporter commented 9 years ago 
Thank you for reporting this issue. We have already made a fix that should 
solve the problem. A new version of PeptideShaker should be available by the 
end of this week.

Original comment by harald.b...@gmail.com on 12 Nov 2014 at 10:30

GoogleCodeExporter commented 9 years ago 
A new version which should fix this issue has been released today, can you 
verify that the data loads now?
Feel free to contact us again should you encounter issues again.

Original comment by mvau...@gmail.com on 14 Nov 2014 at 7:24

GoogleCodeExporter commented 9 years ago 
Thanks for your response. But, same error occuered while loading the 
identification files

...
...
Mon Nov 17 15:04:42 KST 2014        Validating identifications at 1% FDR, 
quality control of matches.
Mon Nov 17 15:05:16 KST 2014        Scoring PTMs in peptides.

Mon Nov 17 15:05:17 KST 2014        Importing Data Canceled!
Mon Nov 17 15:05:17 KST 2014        An error occurred while loading the 
identification files:
Mon Nov 17 15:05:17 KST 2014        Attempting to create duplicate peptide key: 
RIHMEKEMEMKK_15.994915-ATAA-4.
...

Mon Nov 17 14:14:53 KST 2014: PeptideShaker version 0.35.2.
Memory given to the Java virtual machine: 7456948224.
Total amount of memory in the Java virtual machine: 128974848.
Free memory: 110674712.
Java version: 1.8.0_25.
jshortcut.dll loaded via tmp generated pathname: 
C:\Users\JJUN\AppData\Local\Temp\jshortcut-3361852055548497046.dll
1714 script command tokens
(C) 2009 Jmol Development
Jmol Version: 12.0.43  2011-05-03 14:21
java.vendor: Oracle Corporation
java.version: 1.8.0_25
os.name: Windows 7
memory: 37.1/129.0
processors available: 4
useCommandThread: false
<CompomicsError>PeptideShaker processing failed. See the PeptideShaker log for 
details.</CompomicsError>
java.lang.IllegalArgumentException: Attempting to create duplicate peptide key: 
RIHMEKEMEMKK_15.994915-ATAA-4.
    at eu.isas.peptideshaker.ptm.PtmScorer.scorePTMs(PtmScorer.java:842)
    at eu.isas.peptideshaker.ptm.PtmScorer.scorePeptidePtms(PtmScorer.java:1327)
    at eu.isas.peptideshaker.PeptideShaker.processIdentifications(PeptideShaker.java:453)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:540)
    at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:440)
    at javax.swing.SwingWorker$1.call(Unknown Source)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at javax.swing.SwingWorker.run(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
Free memory: 2527906024

.....

please one more check..
Thank you, sir.

Original comment by Jihye.Sh...@gmail.com on 17 Nov 2014 at 7:38

GoogleCodeExporter commented 9 years ago 
Hi and sorry that the problem is not solved as it should. Can you make the data 
available to us so that we look into what went wrong?

Original comment by mvau...@gmail.com on 17 Nov 2014 at 10:48

GoogleCodeExporter commented 9 years ago

Original comment by mvau...@gmail.com on 17 Nov 2014 at 10:49

GoogleCodeExporter commented 9 years ago 
Hi again,

I don't think that we received your data to test? Can you verify that the 
problem still occurs on the latest version and show us how to reproduce the bug 
if it happens again?

Thank you,

Marc

Original comment by mvau...@gmail.com on 23 Jan 2015 at 2:57